We have implemented this utility (converting .WSQ fingerprint file into .BMP) in Java and made it available as a web service. You are free to use it: http://leversystems.com/products/fiss/. Sample code on how to use this service is also available in C# and Java.

Lakota Software Solutions has WSQParse, which is the only pure Java NIST and FBI certified algorithm (see https://www.fbibiospecs.org/WSQ/Implementations/Default.aspx) to encode and decode WSQ images. It is also the fastest algorithm that I have tested. Much faster than the native C versions, such as Aware's WSQ1000 and NIST NBIS WSQ. Their library interfaces directly with ImageIO which makes it very easy to transform to and from WSQ to any other image formats. Also works very well on Android. You can download a free evaluation of their NistParse software, which comes with WSQParse at http://www.lakotasoftware.com/products.